Preparation of a pre-treated biomass stream to benefit hydrolysis and subsequent fermentation are well known in the art. Taherzadeh and Karimi (2007) “Enzyme-based Ethanol”, BioResources 2(4), 707-738 discuss the various pre-treatment processes. In the pre treatment process, the biomass is treated with high pressure, high temperature steam or water and some water is removed. However, according to these authors, one of the goals is to avoid the formation of inhibitory by-products. However, rather than avoid formation, one could remove them. There exists therefore a need to economically remove the by-products of biomass pre-treatment.